[Numpy-discussion] Fwd: Fwd: numpy error with mkl 10.1

akshar bhosale akshar.bhosale@gmail....
Wed Nov 2 22:33:44 CDT 2011


any other means of getting it fixed?

---------- Forwarded message ----------
From: Olivier Delalleau <shish@keba.be>
Date: Thu, Nov 3, 2011 at 8:58 AM
Subject: Re: [Numpy-discussion] Fwd: numpy error with mkl 10.1
To: Discussion of Numerical Python <numpy-discussion@scipy.org>


I'm sorry, I don't know. I'm not at all an expert about numpy installation,
I just happened to have access to a computer with a working install of
numpy with MKL, so I thought it might help... but I'm afraid that's all I
can do for you :/

-=- Olivier

2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>

> thanks once again. how can i use ur distutils directly (ur supplied files
> etc)
>
> On Thu, Nov 3, 2011 at 8:15 AM, Olivier Delalleau <shish@keba.be> wrote:
>
>> Yes they pass:
>>
>> Ran 2030 tests in 6.672s
>>
>> OK (KNOWNFAIL=1)
>> <nose.result.TextTestResult run=2030 errors=0 failures=0>
>>
>> Google "einsum hang".... I know you're not the first one with this bug
>> (but I'm not sure exactly how to fix it).
>>
>> -=- Olivier
>>
>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>
>>>  my numpy.test hangs here
>>>
>>> Test whether equivalent subarray dtypes hash the same. ... ok
>>> Test whether different subarray dtypes hash differently. ... ok
>>> Test some data types that are equal ... ok
>>> Test some more complicated cases that shouldn't be equal ... ok
>>> Test some simple cases that shouldn't be equal ... ok
>>> test_single_subarray (test_dtype.TestSubarray) ... ok
>>> test_einsum_errors (test_einsum.TestEinSum) ... ok
>>> test_einsum_sums_cfloat128 (test_einsum.TestEinSum) ...
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: akshar bhosale <akshar.bhosale@gmail.com>
>>> Date: Thu, Nov 3, 2011 at 8:00 AM
>>> Subject: Re: [Numpy-discussion] numpy error with mkl 10.1
>>> To: Discussion of Numerical Python <numpy-discussion@scipy.org>
>>>
>>>
>>> hi,
>>> on your machine, is numpy.test passed?
>>>
>>>
>>> On Thu, Nov 3, 2011 at 6:54 AM, Olivier Delalleau <shish@keba.be> wrote:
>>>
>>>> I believe they are optional, but I'm not sure.
>>>>
>>>> Note that this system I copied the distutils from is not one I setup
>>>> myself so I'm not sure how numpy was installed exactly. I just know it
>>>> works and it's using MKL :) It's an 8 core Intel(R) Xeon(R) CPU E5462  @
>>>> 2.80GHz (x86_64 as well).
>>>>
>>>> -=- Olivier
>>>>
>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>
>>>>>   hi,
>>>>> are amd,fftw and umfpack required? my architecture is : intel xeon
>>>>> x_86_64.
>>>>>
>>>>> On Thu, Nov 3, 2011 at 6:30 AM, Olivier Delalleau <shish@keba.be>wrote:
>>>>>
>>>>>> It's inside the distutils folder.
>>>>>>
>>>>>> -=- Olivier
>>>>>>
>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>>
>>>>>>> thanks..what about site.cfg?
>>>>>>>
>>>>>>> On Thu, Nov 3, 2011 at 1:27 AM, Olivier Delalleau <shish@keba.be>wrote:
>>>>>>>
>>>>>>>>  Sorry, no clue :/
>>>>>>>>
>>>>>>>> I made a tarball with my distutils folder here:
>>>>>>>> http://www.iro.umontreal.ca/~delallea/tmp/distutils.tar.bz2
>>>>>>>> Hope this helps...
>>>>>>>>
>>>>>>>> -=- Olivier
>>>>>>>>
>>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>>>>
>>>>>>>>>    hi,
>>>>>>>>> thanks for the reply
>>>>>>>>> none of them is linked with libmkl_lapack.so.
>>>>>>>>> what can be the problem?
>>>>>>>>> libmkl_lapack.so is present in its location.
>>>>>>>>>
>>>>>>>>> if possible, can you send your site.cfg and other related files
>>>>>>>>> like intelccompilers.py / system_config.py etc...and configure/build
>>>>>>>>> options, i will try the same?
>>>>>>>>>
>>>>>>>>> On Wed, Nov 2, 2011 at 11:51 PM, Olivier Delalleau <shish@keba.be>wrote:
>>>>>>>>>
>>>>>>>>>>  Hmm that's interesting, it's not linked against libmkl_lapack.
>>>>>>>>>> On my system with MKL it says:
>>>>>>>>>>
>>>>>>>>>> ldd linalg/lapack_lite.so
>>>>>>>>>>         libmkl_lapack.so => /opt/intel/mkl/*MailScanner
>>>>>>>>>> soupçonne le lien suivant d'être une tentative de fraude de la part de
>>>>>>>>>> "10.1.3.027" * *MailScanner soupçonne le lien suivant d'être une
>>>>>>>>>> tentative de fraude de la part de "10.1.3.027" MailScanner
>>>>>>>>>> soupçonne le lien suivant d'être une tentative de fraude de la part de
>>>>>>>>>> "10.1.3.027" MailScanner soupçonne le lien suivant d'être une
>>>>>>>>>> tentative de fraude de la part de "10.1.3.027" MailScanner
>>>>>>>>>> warning: numerical links are often malicious:
>>>>>>>>>> 10.1.3.027/lib/em64t/libmkl_lapack.so*<http://10.1.3.027/lib/em64t/libmkl_lapack.so>(0x00002acf0e25a000)
>>>>>>>>>>         libmkl_intel_lp64.so => /opt/intel/mkl/*MailScanner
>>>>>>>>>> soupçonne le lien suivant d'être une tentative de fraude de la part de
>>>>>>>>>> "10.1.3.027" * *MailScanner soupçonne le lien suivant d'être une
>>>>>>>>>> tentative de fraude de la part de "10.1.3.027" MailScanner
>>>>>>>>>> soupçonne le lien suivant d'être une tentative de fraude de la part de
>>>>>>>>>> "10.1.3.027" MailScanner soupçonne le lien suivant d'être une
>>>>>>>>>> tentative de fraude de la part de "10.1.3.027" MailScanner
>>>>>>>>>> warning: numerical links are often malicious:
>>>>>>>>>> 10.1.3.027/lib/em64t/libmkl_intel_lp64.so*<http://10.1.3.027/lib/em64t/libmkl_intel_lp64.so>(0x00002acf0ebb8000)
>>>>>>>>>>         libmkl_intel_thread.so => /opt/intel/mkl/*MailScanner
>>>>>>>>>> soupçonne le lien suivant d'être une tentative de fraude de la part de
>>>>>>>>>> "10.1.3.027" * *MailScanner soupçonne le lien suivant d'être une
>>>>>>>>>> tentative de fraude de la part de "10.1.3.027" MailScanner
>>>>>>>>>> soupçonne le lien suivant d'être une tentative de fraude de la part de
>>>>>>>>>> "10.1.3.027" MailScanner soupçonne le lien suivant d'être une
>>>>>>>>>> tentative de fraude de la part de "10.1.3.027" MailScanner
>>>>>>>>>> warning: numerical links are often malicious:
>>>>>>>>>> 10.1.3.027/lib/em64t/libmkl_intel_thread.so*<http://10.1.3.027/lib/em64t/libmkl_intel_thread.so>(0x00002acf0ef2e000)
>>>>>>>>>>         libmkl_def.so => /opt/intel/mkl/*MailScanner soupçonne
>>>>>>>>>> le lien suivant d'être une tentative de fraude de la part de "10.1.3.027"
>>>>>>>>>> * *MailScanner soupçonne le lien suivant d'être une tentative de
>>>>>>>>>> fraude de la part de "10.1.3.027" MailScanner soupçonne le lien
>>>>>>>>>> suivant d'être une tentative de fraude de la part de "10.1.3.027" MailScanner
>>>>>>>>>> soupçonne le lien suivant d'être une tentative de fraude de la part de
>>>>>>>>>> "10.1.3.027" MailScanner warning: numerical links are often
>>>>>>>>>> malicious: 10.1.3.027/lib/em64t/libmkl_def.so*<http://10.1.3.027/lib/em64t/libmkl_def.so>(0x00002acf0fc93000)
>>>>>>>>>>         libmkl_core.so => /opt/intel/mkl/*MailScanner soupçonne
>>>>>>>>>> le lien suivant d'être une tentative de fraude de la part de "10.1.3.027"
>>>>>>>>>> * *MailScanner soupçonne le lien suivant d'être une tentative de
>>>>>>>>>> fraude de la part de "10.1.3.027" MailScanner soupçonne le lien
>>>>>>>>>> suivant d'être une tentative de fraude de la part de "10.1.3.027" MailScanner
>>>>>>>>>> soupçonne le lien suivant d'être une tentative de fraude de la part de
>>>>>>>>>> "10.1.3.027" MailScanner warning: numerical links are often
>>>>>>>>>> malicious: 10.1.3.027/lib/em64t/libmkl_core.so*<http://10.1.3.027/lib/em64t/libmkl_core.so>(0x00002acf1080e000)
>>>>>>>>>>
>>>>>>>>>>         libguide.so => /opt/intel/cce/10.1.026/lib/libguide.so
>>>>>>>>>> (0x00002acf10a03000)
>>>>>>>>>>         libpthread.so.0 => /lib64/libpthread.so.0
>>>>>>>>>> (0x00002acf10ba6000)
>>>>>>>>>>         libm.so.6 => /lib64/libm.so.6 (0x00002acf10dc1000)
>>>>>>>>>>         libpython2.6.so.1.0 =>
>>>>>>>>>> /opt/python64/2.6.4/lib/libpython2.6.so.1.0 (0x00002acf11044000)
>>>>>>>>>>         libc.so.6 => /lib64/libc.so.6 (0x00002acf113f3000)
>>>>>>>>>>         libdl.so.2 => /lib64/libdl.so.2 (0x00002acf1174b000)
>>>>>>>>>>         /lib64/ld-linux-x86-64.so.2 (0x0000003d90400000)
>>>>>>>>>>         libutil.so.1 => /lib64/libutil.so.1 (0x00002acf1194f000)
>>>>>>>>>>
>>>>>>>>>> So to clarify, what I was trying to achieve is find which of
>>>>>>>>>> numpy's shared libraries was trying to load libmkl_lapack.so, and if it
>>>>>>>>>> could be found properly with ldd. Just to make sure it's not another .so,
>>>>>>>>>> can you run from within your numpy directory:
>>>>>>>>>>    find -name "*.so" -exec ldd \{} \; | grep lapack
>>>>>>>>>>
>>>>>>>>>> If the output is not empty, try to run ldd on all .so within
>>>>>>>>>> numpy to see which one is linked against libmkl_lapack.so. Then hopefully
>>>>>>>>>> something will stand out (I admit that's not guaranteed though ;).
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> -=- Olivier
>>>>>>>>>>
>>>>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> ldd
>>>>>>>>>>> Python-2.6/lib/python2.6/site-packages/numpy/linalg/lapack_lite.so
>>>>>>>>>>>     libstdc++.so.6 => /usr/lib64/libstdc++.so.6
>>>>>>>>>>> (0x00002b1199349000)
>>>>>>>>>>>     libmkl_def.so =>
>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_def.so
>>>>>>>>>>> (0x00002b1199653000)
>>>>>>>>>>>     libmkl_intel_lp64.so =>
>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_lp64.so
>>>>>>>>>>> (0x00002b119a1a8000)
>>>>>>>>>>>     libmkl_intel_thread.so =>
>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_thread.so
>>>>>>>>>>> (0x00002b119a503000)
>>>>>>>>>>>     libmkl_core.so =>
>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_core.so
>>>>>>>>>>> (0x00002b119b22c000)
>>>>>>>>>>>     libmkl_mc.so =>
>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_mc.so (0x00002b119b420000)
>>>>>>>>>>>     libpthread.so.0 => /lib64/libpthread.so.0
>>>>>>>>>>> (0x00002b119c176000)
>>>>>>>>>>>     libimf.so =>
>>>>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so (0x00002b119c392000)
>>>>>>>>>>>     libsvml.so =>
>>>>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libsvml.so (0x00002b119c6e9000)
>>>>>>>>>>>     libm.so.6 => /lib64/libm.so.6 (0x00002b119c8a6000)
>>>>>>>>>>>     libiomp5.so =>
>>>>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libiomp5.so (0x00002b119cb2b000)
>>>>>>>>>>>     libintlc.so.5 =>
>>>>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libintlc.so.5 (0x00002b119ccbc000)
>>>>>>>>>>>     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b119cdf9000)
>>>>>>>>>>>     libc.so.6 => /lib64/libc.so.6 (0x00002b119d007000)
>>>>>>>>>>>     libdl.so.2 => /lib64/libdl.so.2 (0x00002b119d37e000)
>>>>>>>>>>>     /lib64/ld-linux-x86-64.so.2 (0x0000003fb8000000)
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Nov 2, 2011 at 11:26 PM, Olivier Delalleau <
>>>>>>>>>>> shish@keba.be> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Doh I'm sorry, I forgot the problem was with lapack, what about
>>>>>>>>>>>> ldd numpy/linalg/lapack_lite.so?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>> ldd _dotblas.so
>>>>>>>>>>>>> libstdc++.so.6 => /usr/lib64/libstdc++.so.6
>>>>>>>>>>>>> (0x00002b12f0692000)
>>>>>>>>>>>>>     libmkl_def.so =>
>>>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_def.so
>>>>>>>>>>>>> (0x00002b12f099c000)
>>>>>>>>>>>>>     libmkl_intel_lp64.so =>
>>>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_lp64.so
>>>>>>>>>>>>> (0x00002b12f14f1000)
>>>>>>>>>>>>>     libmkl_intel_thread.so =>
>>>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_intel_thread.so
>>>>>>>>>>>>> (0x00002b12f184c000)
>>>>>>>>>>>>>     libmkl_core.so =>
>>>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_core.so
>>>>>>>>>>>>> (0x00002b12f2575000)
>>>>>>>>>>>>>     libmkl_mc.so =>
>>>>>>>>>>>>> /opt/intel/Compiler/11.0/069/mkl/lib/em64t/libmkl_mc.so (0x00002b12f2769000)
>>>>>>>>>>>>>     libpthread.so.0 => /lib64/libpthread.so.0
>>>>>>>>>>>>> (0x00002b12f34bf000)
>>>>>>>>>>>>>     libimf.so =>
>>>>>>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libimf.so (0x00002b12f36db000)
>>>>>>>>>>>>>     libsvml.so =>
>>>>>>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libsvml.so (0x00002b12f3a32000)
>>>>>>>>>>>>>     libm.so.6 => /lib64/libm.so.6 (0x00002b12f3bef000)
>>>>>>>>>>>>>     libiomp5.so =>
>>>>>>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libiomp5.so (0x00002b12f3e74000)
>>>>>>>>>>>>>     libintlc.so.5 =>
>>>>>>>>>>>>> /opt/intel/Compiler/11.0/069/lib/intel64/libintlc.so.5 (0x00002b12f4005000)
>>>>>>>>>>>>>     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b12f4142000)
>>>>>>>>>>>>>     libc.so.6 => /lib64/libc.so.6 (0x00002b12f4350000)
>>>>>>>>>>>>>     libdl.so.2 => /lib64/libdl.so.2 (0x00002b12f46c7000)
>>>>>>>>>>>>>     /lib64/ld-linux-x86-64.so.2 (0x0000003fb8000000)
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Wed, Nov 2, 2011 at 10:14 PM, Olivier Delalleau <
>>>>>>>>>>>>> shish@keba.be> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Ok, can you print the output of ldd numpy/core/_dotblas.so?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> -=- Olivier
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> HI,
>>>>>>>>>>>>>>> It is already added in the LD_LIBRARY_PATH, thenalso it is
>>>>>>>>>>>>>>> generating the same error.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Wed, Nov 2, 2011 at 10:01 PM, Olivier Delalleau <
>>>>>>>>>>>>>>> shish@keba.be> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Locate your libmkl_lapack.so and try to add the directory
>>>>>>>>>>>>>>>> that contains it to your LD_LIBRARY_PATH environment variable.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> -=- Olivier
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 2011/11/2 akshar bhosale <akshar.bhosale@gmail.com>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> i am getting following error.
>>>>>>>>>>>>>>>>>    python -c 'import numpy;numpy.matrix([[1, 5, 10], [1.0,
>>>>>>>>>>>>>>>>> 3j, 4]],
>>>>>>>>>>>>>>>>>    numpy.complex128).T.I.H'
>>>>>>>>>>>>>>>>>    MKL FATAL ERROR: Cannot load libmkl_lapack.so
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>    have installed numpy 1.6.0 with python 2.6.
>>>>>>>>>>>>>>>>>    i have intel cluster toolkit installed on my system.
>>>>>>>>>>>>>>>>> (11/069 version and mlk=10.1). i have machine having intel xeon processor
>>>>>>>>>>>>>>>>> and rhel 5.2 x86_64
>>>>>>>>>>>>>>>>>    platform.
>>>>>>>>>>>>>>>>> Kindly help
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
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